The LINK-Group was formed in 2004 by researchers and research students from different fields and different universities to discover the topology and dynamics of networks from amino acids to social networks. The group is a multidisciplinary group requiring and offering a multidimensional understanding of complex systems. We use the network approach to judge the importance of our findings by their transferability to another level of complexity (i.e. from proteins to society or vice versa). Moreover, we use networks as "highways" between remote areas of science resolving creativity-deadlocks by allowing the re-formulation of the original questions at a different field and thereby promoting the creative associations by its different conceptual context. The LINK-Group develops novel algorithms to analyze network topology and dynamics and uses them to characterize the adaptation of complex systems to novel environments, and to identify new drug targets. If you want to join us, send your message by clicking here.

Turbine became the best Central European startup

November 2017

Turbine became the best Central European startup + also received the best AI startup award. Turbine was founded together by 4 LINK-members, Kristóf Zsolt Szalay, the inventor of Turbine, Daniel Veres CMO and Ivan Fekete CS, and Peter Csermely as an advisor, as well as by the CEO, Szabolcs Nagy. The award was announced in Sofia, Bulgaria. Congratulations to the whole growing team of close to 30 people by now!

A paper on a general mechanism of network-driven adaptation, learning and decision making processes

November 2017

Csermely Peter's paper on a general mechanism of network-driven adaptation, learning and decision making processes appeared on-line in BioEssays, and is accessible here, or at this web-page. The paper shows that deliberative democracy is an efficient learning strategy developed as the success of a billion-year evolution.

Turbine became the best start-up of the year

September 2017

The Turbine startup became start-up of the year on the Hungary primary of the Central European Startup contest having more than 200 applicants from Hungary. The start-up won alltogether 3 categories in the contest which is rather unprecedented. Congratulations for the growing team having several LINK-Group members! (On the picture the there is the founding team, from left to right: Kristóf Szalay who invented Turbine, Iván Fekete who established the dynamic signaling network used by Turbine, Dániel Veres Chief Medical Officer, Peter Csermely and Szabolcs Nagy, CEO.)

Turbine became the #1 health startup at Pioneers'17 having more than 4000 contestants

June 2017

The Turbine startup became the #1 health startup of the Pioneers 2017 event The event had more than 4000 contestants, whose first 500 were invited to the meeting. Turbine was selected as one of the best 50 and then won the health category. Turbine was founded by several LINK Group members, such as the originator of the idea, Kristóf Szalay CTO, Daniel Veres CMO and Iván Fekete Chief Scientist + last but not least the CEO, Szabolcs Nagy. In 2016 the startup won Bayer's accelerator contest. Currently 2 of the top 10 pharma companies are already using Turbine technology to speed up their pipeline and rationalize R&D decision making.

LINK-Group member, Eszter Arany received a grand-prize at the national round of the 2017. high school student research conference

April 2017

LINK Group member, Eszter Arany with the supervision of Péter Csermely and Aurél Prósz won a grand-prize at the national round of the 2017. high school student research conference (TUDOK). She also won the chance to present her findings at the national round of the university student research conference (OTDK). Congratulations for the hard work!

Réka and István Albert became visiting professors of the Semmelweis University spending their sabbatical at the LINK-Group

February 2017

Réka Albert and István Albert became visiting professors of the Semmelweis University and spend their sabbatical at the LINK-Group.

Awarded lectures of LINK-Group members at recent scientific conferences

February 2017

LINK Group members Eszter Arany, Levente Dobronyi, Iván Fekete, Péter Mendik, István Taisz (together with Gábor Hajdú) with the supervision of Péter Csermely, Eszter Gecse, Aurél Prósz, Csaba Sőti and Dániel Veres won several awards at recent scientific student conferences of the Semmelweis University and the Hungarian Research Student Organization. Congratulations! Keep going!

The Turbine start-up was selected from 405 applicants as one of the 4 winners of Bayer's Grants4Apps accelarator competition

September 2016

The Turbine startup company, founded by several LINK-Group members was selected as one of the four winners of Bayer's 2016 Grants4Apps competition. As part of the benefits, Turbine's founders spend 3 months in Berlin working with Bayer's experts to intitiate a joint project.

LINK-Group member, Aron Ricardo Perez-Lopez, received a silver medal at the 48th International Chemistry Olympiad (IChO)

LINK-Group members established the Turbine start-up to design effective combination therapies with artificial intelligence

October 2015

Several LINK-Group members established a biotech start-up firm, which is based on Kristóf Szalay's formerly developed Turbine network dynamics tool.
Turbine’s built-in artificial intelligence methods predict how e.g. any type of cancer responds to treatment, screening millions of possible drug combinations on a cancer-specific signaling network.
Please find more description at this web-site: http://turbine.hu.

The EntOpt network visualization Cytoscape 3.1 plug-in (http://apps.cytoscape.org/apps/entoptlayout) is
based on the concept of "A unified data representation theory for network visualization, ordering and coarse-graining" published now by István Kovács,
Réka Mizsei and Peter Csermely in Scientific Reports (http://www.nature.com/articles/srep13786).
The plug-in is in beta-phase, so we look for questions and advice to improve it. We are planning to extend the plug-in with hierarchical optimization,
coarse-graining and ordering functions.

17 years-old LINK-Group member, Aron Perez Lopez published a paper on the better human interactome perturbation spreading effects of targets of drugs having side effects

April 2015

Aron Perez Lopez, a 17 years-old member of the LINK Group (http://linkgroup.hu/AronPerez.php)
published a paper accepted in Scientific Reports. The paper shows that in general,
drug targets are better spreaders of perturbations than non-target proteins, and in particular,
targets of drugs with side effects were also better spreaders of perturbations than targets of drugs having no reported side effects in human protein-protein interaction networks.
Colorectal cancer-related proteins were good spreaders and had a high centrality,
while type 2 diabetes-related proteins showed an average spreading efficiency and had an average centrality in the human interactome.
Moreover, the interactome-distance between drug targets and disease-related proteins was higher in diabetes than in colorectal cancer.
These results may help a better understanding of the network position and dynamics of drug targets and disease-related proteins, and may contribute to develop additional,
network-based tests to increase the potential safety of drug candidates.

We have updated our ModuLand plug-in for Cytoscape 3.0

February 2015

Daniel Ábrám completed and uploaded the Cytoscape 3.0-compatible updated version of our modularization program, ModuLand: http://apps.cytoscape.org/apps/moduland20.
The ModuLand method family (PLoS ONE, 7, e12528) is determining and visualizing overlapping network modules (clusters/communities).
The plug-in builds the hierarchy of network modules, where meta-nodes of the higher layer are the modules of the lower layer.
The plug-in also calculates a number of topological measures such as community centrality, bridgeness and overlap, characterizing the centre of modules, as well as intermodular nodes (bridges) between two or more modules. More info here: www.modules.linkgroup.hu

Máté-Szalay Bekő completed and uploaded the EntOpt network visualization Cytoscape 3.1 plug-in (http://apps.cytoscape.org/apps/entoptlayout),
which is based on the concept of "A unified data representation theory for network visualization, ordering and coarse-graining" published earlier by István Kovács, Réka Mizsei and Peter Csermely as a pre-print (http://arxiv.org/abs/1409.8420).
The plug-in is in beta-phase, so Máté is looking for all questions and advice to improve it. We are planning to extend the plug-in with hierarchical optimization, coarse-graining and ordering functions..

Kristóf Zsolt Szalay and his Turbine toolkit won the Semmelweis Innovation Award 2015

January 2015

We are happy to announce that the winner of the annual Semmelweis Innovation Award in the PhD work category is Kristóf Zsolt Szalay and his Turbine network dynamics toolkit!

Kristóf is going to hold a lecture with the title "Dinamikus hálózatelemzés és ami mögötte van" at the Semmelweis Innovation Day.

ComPPI has been accepted for publication in the NAR Database Issue 2015

October 2014

Our paper "ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis"
describing the ComPPI database has been accepted for publication in the Nucleic Acids Research Database Issue 2015.

Turbine wins one of the best poster awards at Interdisciplinary Signaling Workshop 2014

July 2014

The poster "Turbine: Novel dynamic analyses of signaling (and other) networks" by Kristóf Zsolt Szalay and Peter Csermely has won the Best poster award in the Network tools and resources section of the Interdisciplinary Signaling Workshop 2014.

Best interdisciplinary signaling team award

July 2014

The team working on the topic "Can we create large-scale signaling networks?" originating from the LINK-Group at the Interdisciplinary Signaling Workshop 2014 has won the Best interdisciplinary signaling team award!

Members of the group were:

Andrei Zinovyev (team leader, Institut Curie)

Katja Rybakova (presenter, UC Dublin)

Kristóf Zsolt Szalay (topic owner, LINK-Group)

Rune Linding (DTU)

Ana Mitrovic (University of Ljubljana)

Dénes Türei (NetBiol)

András Zeke (ELTE TTK)

Leilei Zhong (MIRA Institute)

More than 100,000 visitors of the LINK-Group web-site

June 2014

We would like to thank to our more than 100,000 visitors at this web-site.
We continue to add new algorithms, resources, papers, lectures and other information to the site. Please share your comments with us here: http://linkgroup.hu/email.php

Description of Turbine 1.4, an extensive tool for the analysis of network perturbations and dynamics was published in PLoS ONE

September 2013

Turbine 1.4 is an open-source network analysis package for simulating network dynamics. It is particularly suited for experiments involving perturbations (i.e.: observing the effects of outside stimulations on a target network). Turbine is written in C++, and is currently available for Windows and Linux systems. Turbine is able to accommodate any model or real world networks, single, multiple, or continuous perturbations with custom-made delay or dissipation dynamics. You may see a more detailed characterization of the program and download all its components, source code, and detailed instructions here.The PLoS ONE paper describing the results obtained by Turbine can be accessed here: Download the document!

Description of NetworGame 2.0, a program package to simulate spatial games on model and real world networks with individual starting strategies of any nodes was published in PLoS ONE

Our comprehensive review on the use of networks in drug design was published in Pharmacology & Therapeutics and was recommended 2 times as an F1000 Prime paper

May 2013

A comprehensive review on the topology and dynamics of networks was published in Pharmacology & Therapeutics and was recommended 2 times at the maximum, 3-star level as an F1000 Prime paper.

In the review we cited 1270 references, and gave extensive examples on the use of network approach in drug design. Several novel concepts were formulated, including the concept of the "central hit strategy", which selectively targets central node/edges of the flexible networks of infectious agents or cancer cells to kill them. On the contrary, the "network influence strategy" works against other diseases, where an efficient reconfiguration of rigid networks needs to be achieved. The review can be downloaded from here.

Peter Csermely was elected as a member of the Hungarian Academy of Sciences

May 2013

The LINK-member, Peter Csermely was elected as a member of the Hungarian Academy of Sciences. The Academy was established in 1825, covers all areas of science and the number of its members younger than 70 years can not be higher than 200.

A Cytoscape plug-in of the ModuLand modularization program was published in Bioinformatics

August 2012

An updated version of the user-friendly, platform independent implementation of the LinkLand method of the ModuLand method family published earlier in PLoS ONEbecame available as a plug-in for the widely used Cytoscape program. The paper introducing the plug-in was published in Bioinformatics and can be accessed here. The introducing paper demonstrates the usefulness of the method

to identify an extensively overlapping modular structure;

to define a modular core and hierarchy allowing an easier functional annotation;

to identify key nodes of high community centrality, modular overlap or bridgeness in protein structure, protein-protein interaction and metabolic networks.

A joint paper with Ruth Nussinov on the new drug-design paradigm of allo-network drugs was published as the cover story of the December issue of Trends in Pharmacological Sciences

November 2011

The paper proposed that the concept of allosteric drugs can be broadened to allo-network drugs, whose effects can propagate either within a protein, or across several proteins, to enhance or inhibit specific interactions along a pathway. Allo-network drugs can achieve specific, limited changes at the systems level, and in this way can achieve fewer side effects and lower toxicity. The paper summarized possible methods to identify allo-network drug targets and sites. The concept outlined a new paradigm in systems-based drug design. The paper, which was published as the cover story of the December issue of Trends in Pharmacological Sciences, can be downloaded from here.

Ágoston Mihalik's paper showing a partial desintegration of the yeast interactome as a general model of systems level adatptation processes has been published in PLoS Computational Biology

July 2011

The paper described that heat shock induces a marked decrease in the overlap of the communities (modules) of the yeast interactome. Our results indicated that heat shock induces a partial disintegration of the protein-protein interaction network. The residual inter-modular bridges, maintaining the integrity of the interactome after stress, were key proteins of stress-survival. The changes observed may be rather general occurring at the initial phase of crises in many complex systems, such as proteins in physical stretch, ecosystems in abrupt environmental changes or social networks in economic crisis. De-coupling and re-wiring of modules emerges as a general model of adaptation and learning. The paper and its Supplement, which were published in PLoS Computational Biology, can be downloaded from here.

The Hungarian version of the book Weak Links was voted to the best 500 Hungarian books

June 2011

A wide panel of experts has recently determined the “Márai-list”, which is a list of the top 500 Hungarian books (including the top 250 non-fiction books) among a competing 8,000 books recommended to all Hungarian libraries. The Hungarian version of the book Weak Links (a 2009 Springer book on networks, which is downloadable from here or at Google) has been included to this selection of the top 250 non-fiction Hungarian books.

A summary paper of our results appeared in Science Signaling: Network-based tools in the identification of novel drug-targets

May 2011

A summary paper and an accompanying slide show of our work appeared in the May 2011 issue of Science Signaling. Slides were updated from the opening presentation at the International Conference on Systems Biology of Human Disease (SBHD) in Boston, Massachusetts, 16 to 18 June 2010. The paper contains several novel ideas on network dynamics and drug design, a summary of our very recent results as well as a brief description of a few ongoing projects. The paper is available here and the accompanying slideshow is downloadable from here.